A key aim of biotechnology and nanotechnology is the construction of new biomaterials, including individual geometrical objects, nanomechanical devices, and extended constructions that permit the fabrication of intricate structures of materials to serve many practical purposes (Feynman et al., Miniaturization 282–296 (1961); Drexler, Proc. Nat. Acad. Sci. (USA) 78:5275–5278 (1981); Robinson et al., Prot Eng 1 295–300 (1987); Seeman, DNA & Cell Biol. 10:475–486 (1991); Seeman, Nanotechnol 2:149–159 (1991)). Molecules of biological systems, for example, nucleic acids, have the potential to serve as building blocks for these constructions due to their self and programmable-assembly capabilities.
DNA molecules possess a distinct set of mechanical, physical, and chemical properties. From a mechanical point of view, DNA molecules can be rigid (e.g., when the molecules are less than 50 nm, the persistent length of double stranded DNA (Bouchiat, C. et al., Biophys J 76:409–13 (1999); Tinland et al., Macromolecules 30:5763–5765 (1997); Toth et al., Biochemistry 37:8173–9 (1998)), or flexible. Physically, DNA is small, with a width of about 2 nanometers and a length of about 0.34 nanometers per basepair (for B-DNA). In nature, DNA can be found in either linear or circular shapes. Chemically, DNA is generally stable, non-toxic, water soluble, and is commercially available in large quantities and in high purity. Moreover, DNA molecules are easily and highly manipulable by various well-known enzymes such as restriction enzymes and ligases. Also, under proper conditions, DNA molecules will self-assemble with complementary strands of nucleic acid (e.g., DNA, RNA, or Peptide Nucleic Acid, (PNA)), proteins or peptides. Furthermore, DNA molecules can be amplified exponentially and ligated specifically. Thus, DNA is an excellent candidate for constructing nano-material.
The concept of using DNA molecules for non-genetic application has only recently emerged as two new fields of research: DNA-computation, such as using DNA as algorithms for solving combinatorial problems (Adleman, Science 266:1021–4 (1994); Guarnieri et al., Science 273:220–3 (1996); Ouyang et al., Science 278:446–9 (1997); Sakamoto et al., Science 288:1223–6 (2000); Benenson et al., Nature 414:430–4 (2001)), and DNA-nanotechnology, such as using DNA molecules for nano-scaled frameworks and scaffolds (Niemeyer, Applied Physics a-Materials Science & Processing 68:119–124 (1999); Seeman, Annual Review of Biophysics and Biomolecular Structure 27:225–248 (1998)). However, the design and production of DNA-based materials is still problematic (Mao et al., Nature 397:144–146 (1999); Seeman et al., Proc Natl Acad Sci USA 99:6451–6455 (2002); Yan et al., Nature 415:62–5 (2002); Mirkin et al., Nature 382:607–9 (1996); Watson et al., J Am Chem Soc 123:5592–3 (2001)). For example, previously reported nucleic acid structures were quite polydispersed with flexible arms and self-ligated circular and non-circular byproducts (Ma et al., Nucleic Acids Res 14:9745–53 (1986); Wang et al., Journal of the American Chemical Society 120:8281–8282 (1998); Nilsen et al., J Theor Biol 187:273–84 (1997)), which severely limited their utility in constructing DNA materials. The yield and purity of those structures were also unknown.
Alderman first solved an instance of the directed Hamiltonian path problem using DNA molecules and reactions (Adleman, Science 266:1021–4 (1994)). Since then, DNA has been used as algorithms for solving combinatorial problems (Guarnieri et al., Science 273:220–3 (1996); Ouyang et al., Science 278:446–9 (1997); Sakamoto et al., Science 288:1223–6 (2000); Benenson et al., Nature 414:430–4 (2001)) and logical computation (Mao et al., Nature 407:493–6 (2000)). However, in all of these applications, the shapes of DNA molecules have not been altered; they are still in linear form as the hair-pin form was employed, which is also a linear form.
The field of DNA nanotechnology was pioneered by Seeman (Seeman, J Biomol Struct Dyn 8:573–81 (1990); Seeman, Accounts of Chemical Research 30:357–363 (1997); Seeman, Trends in Biotechnology 17:437–443 (1999)). Using rigid “crossover” DNA as building blocks, motifs were constructed (Seeman et al., Biophysical Journal 78:308a–308a (2000); Sha et al., Chemistry & Biology 7:743–751 (2000); LaBean et al., Journal of the American Chemical Society 122:1848–1860 (2000); Yang et al., Journal of the American Chemical Society 120:9779–9786 (1998); Mao et al., Nature 386:137–138 (1997)). A DNA mechanical device was also reported (Mao et al., Journal of the American Chemical Society 121:5437–5443 (1999); Yan et al., Nature 415:62–5 (2002)). However, the building blocks and motifs employed so far are isotropic multivalent, possibly useful for growing nano-scaled arrays and scaffolds (Winfree et al., Nature 394:539–44 (1998); Niemeyer, Applied Physics a-Materials Science & Processing 68:119–124 (1999); Seeman, Annual Review of Biophysics and Biomolecular Structure 27:225–248 (1998)), but not suitable for controlled growth, such as in dendrimer, or in creating a large quantity of monodispersed new materials, which are important to realize nucleic acid-based materials.
Other schemes of nano-construction using linear DNA molecules were also reported, including a biotin-avidin based DNA network (Luo, “Novel Crosslinking Technologies to Assess Protein-DNA Binding and DNA-DNA Complexes for Gene Delivery and Expression” (Dissertation). Molecular, Cellular, and Developmental Biology Program, The Ohio State University (1997)), nanocrystals (Alivisatos et al., Nature 382:609–11 (1996)), DNA-protein nanocomplexes (Niemeyer et al., Angewandte Chemie-International Edition 37:2265–2268 (1998)), a DNA-fueled molecular machine (Yurke et al., Nature 406:605–8 (2000)), DNA-block copolymer conjugates (Watson et al., J Am Chem Soc 123:5592–3 (2001)), DNA-silver-wire (Braun et al., Nature 391:775–8 (1998)), and DNA-mediated supramolecular structures (Taton et al., Journal of the American Chemical Society 122:6305–6306 (2000)). In addition, Mirkin has reported DNA sensing via gold nanoparticles (Elghanian et al., Science 277:1078–81 (1997)) and DNA patterning via dip-pen nanolithography (Demers et al., Science 296:1836–8 (2002)), although such patterning is not suitable for large scale production. Recently Mirkin's group reported a DNA array-based detection method that utilized microelectrodes, opening up possibilities for DNA-nanowires (Park et al., Science 295:1503–1506 (2002)). DNA-based lithography was recently reported by Braun's group where linear and very long DNA molecules were reported to serve as masks and RecA proteins served as resists (Keren et al., Science 297:72–5 (2002)). Recently, a small chemical, tris-linker, was reportedly reacted with 5′-hydrazide-modified oligonucleotides in the presence of the 3′-tris-oligonucleotidyl template to allegedly create tri-valent, Y-shape DNA molecules (Eckardt et al., Nature 420:286 (2002)). However, all of these examples involved linear DNA.
Therefore, there is a need for nucleic acid-based materials and for methods to construct these materials.